diff bam_stat.xml @ 49:6b33e31bda10 draft

Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2

--- a/bam_stat.xml	Tue Apr 21 10:27:06 2015 -0400
+++ b/bam_stat.xml	Thu Jul 16 17:43:43 2015 -0400
@@ -1,31 +1,49 @@
-<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4">
+<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4galaxy1">
     <description>
         reads mapping statistics for a provided BAM or SAM file.
     </description>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="2.4">rseqc</requirement>
-    </requirements>s
-    <command>
-        bam_stat.py -i $input -q $mapqual 2> $output
+        <expand macro="requirement_package_numpy" />
+        <expand macro="requirement_package_rseqc" />
+    </requirements>
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[bam_stat.py --version]]></version_command>
+
+    <command><![CDATA[
+        bam_stat.py -i $input -q $mapq 2> $output
+        ]]>
     </command>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
-        <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
-    </stdio>
+
     <inputs>
-        <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
-        <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
+        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
+        <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
     </inputs>
+
     <outputs>
         <data format="txt" name="output" />
     </outputs>
-    <help>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            <output name="output" file="bamstats.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
 bam_stat.py
 +++++++++++
 
 This program is used to calculate reads mapping statistics from provided BAM
-file.  This script determines "uniquely mapped reads" from `mapping quality`_,
+file.  This script determines "uniquely mapped reads" from `mapping quality
+<http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
 which quality the probability that a read is misplaced (Do NOT confused with
 sequence quality, sequence quality measures the probability that a base-calling
 was wrong) .
@@ -37,7 +55,7 @@
 	Alignment file in BAM/SAM format.
 
 Minimum mapping quality
-	Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30)
+	Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
 
 Output
 ++++++++++++++
@@ -49,9 +67,10 @@
 
 -----
 
-About RSeQC 
+About RSeQC
 +++++++++++
 
+
 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
 
 The RSeQC package is licensed under the GNU GPL v3 license.
@@ -59,7 +78,9 @@
 .. image:: http://rseqc.sourceforge.net/_static/logo.png
 
 .. _RSeQC: http://rseqc.sourceforge.net/
-.. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
 
+]]>
     </help>
+
+    <expand macro="citations" />
 </tool>